Please add genome option to the pipeline

JetBrains-Research / scasat-smk-pipeline

Single cell ATAC-Seq Snakemake pipeline

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Please add genome option to the pipeline #2

Closed olegs closed 5 years ago

dievsky commented 5 years ago

Unfortunately, the mappability blacklist removal step requires a hardcoded path to the specific blacklist. We could outsource the blacklist download to the user, though, mentioning it in the readme.

dievsky commented 5 years ago

For example, for hg19 it's http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz , and for mm9 it's http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm9-mouse/mm9-blacklist.bed.gz .

dievsky commented 5 years ago

Oh, and the clean_bams rule requires a list of "regular" chromosomes, which would also vary with the genome build. So, the simplest way around this is:

pass the configuration properties via YAML file, since there too many now;
pass the genome build, path to blacklist and the list of regular chromosomes via config;
add a sample config file for user's convenience.

dievsky commented 5 years ago

Moved the configuration properties to config.yaml, provided an example of config and instructions on how to edit it.